diff --git a/plugins/GSdx/GSTextureCache.cpp b/plugins/GSdx/GSTextureCache.cpp
index 81d4406a8d..f17a313f51 100644
--- a/plugins/GSdx/GSTextureCache.cpp
+++ b/plugins/GSdx/GSTextureCache.cpp
@@ -128,7 +128,16 @@ GSTextureCache::Source* GSTextureCache::LookupSource(const GIFRegTEX0& TEX0, con
 			Target* t = *i;
 
 			if(t->m_used && t->m_dirty.empty()) {
-				if (GSUtil::HasSharedBits(bp, psm, t->m_TEX0.TBP0, t->m_TEX0.PSM)) {
+				// Typical bug (MGS3 blue cloud):
+				// 1/ RT used as 32 bits => alpha channel written
+				// 2/ RT used as 24 bits => no update of alpha channel
+				// 3/ Lookup of texture that used alpha channel as index, HasSharedBits will return false
+				//    because of the previous draw call format
+				//
+				// Solution: consider the RT as 32 bits if the alpha was used in the past
+				uint32 t_psm = (t->m_dirty_alpha) ? t->m_TEX0.PSM & ~0x1 : t->m_TEX0.PSM;
+
+				if (GSUtil::HasSharedBits(bp, psm, t->m_TEX0.TBP0, t_psm)) {
 					if (psm == PSM_PSMT8) {
 						// It is a complex to convert the code in shader. As a reference, let's do it on the CPU, it will
 						// be slow but
@@ -243,6 +252,9 @@ GSTextureCache::Target* GSTextureCache::LookupTarget(const GIFRegTEX0& TEX0, int
 		GL_CACHE("TC: Lookup Target(%s) %dx%d, hit: %d (0x%x, F:0x%x)", to_string(type), w, h, dst->m_texture->GetID(), bp, TEX0.PSM);
 
 		dst->Update();
+
+		dst->m_dirty_alpha |= (TEX0.PSM != PSM_PSMCT24) && (TEX0.PSM != PSM_PSMZ24);
+
 	} else if (CanConvertDepth()) {
 
 		int rev_type = (type == DepthStencil) ? RenderTarget : DepthStencil;
@@ -1303,6 +1315,7 @@ GSTextureCache::Target::Target(GSRenderer* r, const GIFRegTEX0& TEX0, uint8* tem
 {
 	m_TEX0 = TEX0;
 	m_32_bits_fmt |= !(TEX0.PSM & 2);
+	m_dirty_alpha = (TEX0.PSM != PSM_PSMCT24) && (TEX0.PSM != PSM_PSMZ24);
 
 	m_valid = GSVector4i::zero();
 }
diff --git a/plugins/GSdx/GSTextureCache.h b/plugins/GSdx/GSTextureCache.h
index dc679bf345..d3e2ff68f3 100644
--- a/plugins/GSdx/GSTextureCache.h
+++ b/plugins/GSdx/GSTextureCache.h
@@ -82,6 +82,7 @@ public:
 		GSDirtyRectList m_dirty;
 		GSVector4i m_valid;
 		bool m_depth_supported;
+		bool m_dirty_alpha;
 
 	public:
 		Target(GSRenderer* r, const GIFRegTEX0& TEX0, uint8* temp, bool depth_supported);